Nice that it works for you!

My best wishes for your project.

thanks for the explanations and possible solutions.
adam

When you use the Extrude Tool, have the Create Cap option off. It might be helpful for the first extrude to create a closed object, but if left on, each following use on the same polygon selection will create these inside caps.

Those extra Polygons can create a lot of problems. Since it is not simple to filter those out, in general, sometimes it helps to use the
Attribute Manager> Mode> Modeling> Model Check: Select (>>) Non Manifold

This will select the edges if the Shift key is held from Edge to Polygon mode; these polygons are often selected and can be deleted. Not always successful!

With less detailed models and no time for a manual fix, putting those objects into a Volume/Mesher setup and then into a Remesher (perhaps set to 1% even) might create some usable results.

All the best

I think i might just try re-making the model. The main problem i have is that when i have used the extrude tool to push and pull panels (its a spaceship model) its created extra geometry on the inside of the model. then when i come to split the model into smaller sections its impossible to patch the gaps as there are loads of extra layers around the edge that all need to be covered.

I think this is one of those live and learn experiences!!

If it is just unused unconnected Points, then the Mesh> Remove> Optimize function should work.

For print, I think it is safe to say that you have a connected water-tight mesh.
This means you can select a point and use the Select connected.
Then, use (also in the Select Menu) the Hide Selected. Which should show you all "leftovers" inside the object. Then: Show All.

If the inside is connected to the surface, that must be handled manually.

Also, explore the Attribute Manager> Mode> Modeling> Meshcheck options.

Besides that, depending on your Model and details, the Remesh might help or the Volume, perhaps even first, then the other in a sequence.
Case dependent.

If you can share a model via Dropbox, Google, Adobe, Apple, or Wetransfer, as a downloadable option, I can look at it.

Typically, ZBrush has better options for 3D Printing.

All the best